R Notebook

library(data.table)

Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
data.table 1.15.4 using 16 threads (see ?getDTthreads).  Latest news: r-datatable.com

meta <- fread('/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/Descr_matr.txt', sep = '\t', quote = FALSE)
exp_dir <- '/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO'


meta$Samples_Identifier <- sub(pattern = '(S)(0+)(\\d+)',replacement = '\\1\\3', x = meta$Samples_Identifier)
meta$N <- NULL
rownames(meta) <- meta$Samples_Identifier


org1 = 'cho'
org2 = 'human'
count_files <- file.path(exp_dir, paste(meta$Samples_Identifier,org1, org2, sep= '_'), paste(org1, 'counts', sep = '_'), 'counts.txt')

all_counts <- list()

for (x in count_files) {
  counts <- fread(x, stringsAsFactors = F, header = TRUE)
  rownames(counts) <- counts$Geneid
  sample_id <- sub(pattern = paste0(exp_dir, '/(\\w+)_', org1, '_', org2,'/cho_counts/counts.txt'), replacement = '\\1', x = x)
  org1_genes <- startsWith(x = counts$Chr,prefix = org1)
  names(counts) <- c(names(counts)[-ncol(counts)], sample_id)
  print('=================')
  print(paste('SAMPLE: ', sample_id))
  print('------------------')
  print( paste('org1 genes :', sum(org1_genes)))
  print(paste('org1 expression :', sum(counts[org1_genes,][[sample_id]])))
  print(paste('org2 expression :', sum(counts[!org1_genes,][[sample_id]])))
 
  all_counts[[sample_id]]<-counts[org1_genes,][[sample_id]] 
}

[1] "================="
[1] "SAMPLE:  S1"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45942491"
[1] "org2 expression : 7554"
[1] "================="
[1] "SAMPLE:  S2"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38618719"
[1] "org2 expression : 6999"
[1] "================="
[1] "SAMPLE:  S3"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38846899"
[1] "org2 expression : 9216"
[1] "================="
[1] "SAMPLE:  S4"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38066759"
[1] "org2 expression : 6924"
[1] "================="
[1] "SAMPLE:  S5"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47305022"
[1] "org2 expression : 6321"
[1] "================="
[1] "SAMPLE:  S6"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43632489"
[1] "org2 expression : 9224"
[1] "================="
[1] "SAMPLE:  S7"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 49366356"
[1] "org2 expression : 7338"
[1] "================="
[1] "SAMPLE:  S8"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 52292057"
[1] "org2 expression : 6708"
[1] "================="
[1] "SAMPLE:  S9"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47123493"
[1] "org2 expression : 7245"
[1] "================="
[1] "SAMPLE:  S10"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45841459"
[1] "org2 expression : 6466"
[1] "================="
[1] "SAMPLE:  S11"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45398096"
[1] "org2 expression : 6856"
[1] "================="
[1] "SAMPLE:  S12"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 44242769"
[1] "org2 expression : 6100"
[1] "================="
[1] "SAMPLE:  S13"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45984636"
[1] "org2 expression : 5733"
[1] "================="
[1] "SAMPLE:  S14"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43979315"
[1] "org2 expression : 6142"
[1] "================="
[1] "SAMPLE:  S15"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40342333"
[1] "org2 expression : 7348"
[1] "================="
[1] "SAMPLE:  S16"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 39624798"
[1] "org2 expression : 5926"
[1] "================="
[1] "SAMPLE:  S17"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 39280085"
[1] "org2 expression : 6647"
[1] "================="
[1] "SAMPLE:  S18"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 34987062"
[1] "org2 expression : 5941"
[1] "================="
[1] "SAMPLE:  S19"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40416377"
[1] "org2 expression : 5914"
[1] "================="
[1] "SAMPLE:  S20"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38049108"
[1] "org2 expression : 5408"
[1] "================="
[1] "SAMPLE:  S21"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43223541"
[1] "org2 expression : 5164"
[1] "================="
[1] "SAMPLE:  S22"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 46344475"
[1] "org2 expression : 7271"
[1] "================="
[1] "SAMPLE:  S23"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 48471492"
[1] "org2 expression : 7319"
[1] "================="
[1] "SAMPLE:  S24"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 33026929"
[1] "org2 expression : 5867"
[1] "================="
[1] "SAMPLE:  S25"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47665791"
[1] "org2 expression : 7381"
[1] "================="
[1] "SAMPLE:  S26"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43888933"
[1] "org2 expression : 6806"
[1] "================="
[1] "SAMPLE:  S27"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 35496433"
[1] "org2 expression : 6270"
[1] "================="
[1] "SAMPLE:  S28"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 44832127"
[1] "org2 expression : 6130"
[1] "================="
[1] "SAMPLE:  S29"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 42442421"
[1] "org2 expression : 6307"
[1] "================="
[1] "SAMPLE:  S30"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 37114723"
[1] "org2 expression : 9613"
[1] "================="
[1] "SAMPLE:  S31"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 36104009"
[1] "org2 expression : 9893"
[1] "================="
[1] "SAMPLE:  S32"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40277699"
[1] "org2 expression : 10491"

all_counts <- as.data.frame(all_counts)
rn <-counts[org1_genes,]$Geneid
rownames(all_counts) <- rn

rowdata <- data.frame(ncbiRefSeq = rn, row.names = rn)
coldata <- meta


saveRDS(list(counts = all_counts, rowdata = rowdata, coldata = coldata), file = '/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/all_expr_data.rds')

org1 = 'cho'
org2 = 'human'
count_files <- file.path(exp_dir, paste(meta$Samples_Identifier,org1, org2, sep= '_'), paste(org1, 'counts', sep = '_'), 'counts.txt')

all_counts <- list()

for (x in count_files) {
  counts <- fread(x, stringsAsFactors = F, header = TRUE)
  rownames(counts) <- counts$Geneid
  sample_id <- sub(pattern = paste0(exp_dir, '/(\\w+)_', org1, '_', org2,'/cho_counts/counts.txt'), replacement = '\\1', x = x)
  org1_genes <- startsWith(x = counts$Chr,prefix = org1)
  names(counts) <- c(names(counts)[-ncol(counts)], sample_id)
  print('=================')
  print(paste('SAMPLE: ', sample_id))
  print('------------------')
  print( paste('org1 genes :', sum(org1_genes)))
  print(paste('org1 expression :', sum(counts[org1_genes,][[sample_id]])))
  print(paste('org2 expression :', sum(counts[!org1_genes,][[sample_id]])))
 
  all_counts[[sample_id]]<-counts[org1_genes,][[sample_id]] 
}

[1] "================="
[1] "SAMPLE:  S1"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45942491"
[1] "org2 expression : 7554"
[1] "================="
[1] "SAMPLE:  S2"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38618719"
[1] "org2 expression : 6999"
[1] "================="
[1] "SAMPLE:  S3"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38846899"
[1] "org2 expression : 9216"
[1] "================="
[1] "SAMPLE:  S4"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38066759"
[1] "org2 expression : 6924"
[1] "================="
[1] "SAMPLE:  S5"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47305022"
[1] "org2 expression : 6321"
[1] "================="
[1] "SAMPLE:  S6"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43632489"
[1] "org2 expression : 9224"
[1] "================="
[1] "SAMPLE:  S7"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 49366356"
[1] "org2 expression : 7338"
[1] "================="
[1] "SAMPLE:  S8"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 52292057"
[1] "org2 expression : 6708"
[1] "================="
[1] "SAMPLE:  S9"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47123493"
[1] "org2 expression : 7245"
[1] "================="
[1] "SAMPLE:  S10"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45841459"
[1] "org2 expression : 6466"
[1] "================="
[1] "SAMPLE:  S11"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45398096"
[1] "org2 expression : 6856"
[1] "================="
[1] "SAMPLE:  S12"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 44242769"
[1] "org2 expression : 6100"
[1] "================="
[1] "SAMPLE:  S13"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 45984636"
[1] "org2 expression : 5733"
[1] "================="
[1] "SAMPLE:  S14"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43979315"
[1] "org2 expression : 6142"
[1] "================="
[1] "SAMPLE:  S15"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40342333"
[1] "org2 expression : 7348"
[1] "================="
[1] "SAMPLE:  S16"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 39624798"
[1] "org2 expression : 5926"
[1] "================="
[1] "SAMPLE:  S17"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 39280085"
[1] "org2 expression : 6647"
[1] "================="
[1] "SAMPLE:  S18"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 34987062"
[1] "org2 expression : 5941"
[1] "================="
[1] "SAMPLE:  S19"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40416377"
[1] "org2 expression : 5914"
[1] "================="
[1] "SAMPLE:  S20"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 38049108"
[1] "org2 expression : 5408"
[1] "================="
[1] "SAMPLE:  S21"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43223541"
[1] "org2 expression : 5164"
[1] "================="
[1] "SAMPLE:  S22"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 46344475"
[1] "org2 expression : 7271"
[1] "================="
[1] "SAMPLE:  S23"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 48471492"
[1] "org2 expression : 7319"
[1] "================="
[1] "SAMPLE:  S24"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 33026929"
[1] "org2 expression : 5867"
[1] "================="
[1] "SAMPLE:  S25"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 47665791"
[1] "org2 expression : 7381"
[1] "================="
[1] "SAMPLE:  S26"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 43888933"
[1] "org2 expression : 6806"
[1] "================="
[1] "SAMPLE:  S27"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 35496433"
[1] "org2 expression : 6270"
[1] "================="
[1] "SAMPLE:  S28"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 44832127"
[1] "org2 expression : 6130"
[1] "================="
[1] "SAMPLE:  S29"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 42442421"
[1] "org2 expression : 6307"
[1] "================="
[1] "SAMPLE:  S30"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 37114723"
[1] "org2 expression : 9613"
[1] "================="
[1] "SAMPLE:  S31"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 36104009"
[1] "org2 expression : 9893"
[1] "================="
[1] "SAMPLE:  S32"
[1] "------------------"
[1] "org1 genes : 31817"
[1] "org1 expression : 40277699"
[1] "org2 expression : 10491"

all_counts <- as.data.frame(all_counts)
rn <-counts[org1_genes,]$Geneid
rownames(all_counts) <- rn

rowdata <- data.frame(ncbiRefSeq = rn, row.names = rn)
coldata <- meta


saveRDS(list(counts = all_counts, rowdata = rowdata, coldata = coldata), file = '/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/all_expr_data.rds')

pca_plots <- list()

library(DESeq2)

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
    rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs,
    colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds,
    colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
    rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads,
    rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2,
    rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for
    packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

dds <- DESeqDataSetFromMatrix(all_counts, colData = coldata, design=~1)
dds <- DESeq(dds)

Warning in DESeq(dds) :
  the design is ~ 1 (just an intercept). is this intended?
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 104 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

rld <- rlogTransformation(dds)

rlog() may take a few minutes with 30 or more samples,
vst() is a much faster transformation

library(PCAtools)

Loading required package: ggplot2
RStudio Community is a great place to get help: https://community.rstudio.com/c/tidyverse
Loading required package: ggrepel

Attaching package: ‘PCAtools’

The following objects are masked from ‘package:stats’:

    biplot, screeplot

pcaData <- PCAtools::pca(counts(dds, normalized = TRUE), metadata=coldata) 
pca_plots$all_counts_normalized <- biplot(pcaData, colby = "Genotype", shape = "Engulfment", legendPosition = "right") + ggtitle("All samples all counts deseq normalized")
plot(pca_plots$all_counts_normalized)

Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider increasing max.overlaps

pcaData <- PCAtools::pca(assay(rld), metadata=coldata) 
pca_plots$rlog_all <- biplot(pcaData, colby = "Genotype",  shape = "Engulfment", legendPosition = "right") + ggtitle("All samples all counts rlog")
plot(pca_plots$rlog_all)

library(data.table)
bad_samples <- c("S24", "S31", "S27")
coldata <- as.data.frame(coldata[!coldata$Samples_Identifier %in% bad_samples, ])
rownames(coldata) <- coldata$Samples_Identifier
all_counts <- all_counts[, ! colnames(all_counts) %in% bad_samples]

coldata$Genotype <- factor(coldata$Genotype, levels = c("WT", "KO"))
coldata$Engulfment <- factor(coldata$Engulfment, levels = c("alone", "eating"))
coldata$time <- factor(coldata$time, levels = c("2h","4h")) 
coldata$Conditions <- relevel(factor(coldata$Conditions), ref = "ctrl_alone_4h")
coldata$treatment <- paste(coldata$Engulfment, coldata$time, sep= "_")
coldata$treatment <- relevel(factor(coldata$treatment), ref = "alone_4h")
dds <- DESeqDataSetFromMatrix(all_counts, colData = coldata, design=~Conditions)
smallestGroupSize <- 3
keep <- rowSums(counts(dds) >= 10) >= smallestGroupSize
dds <- dds[keep,]
dds <- DESeq(dds)

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

rld <- rlogTransformation(dds)
library(PCAtools)
pcaData <- PCAtools::pca(counts(dds, normalized = TRUE), metadata=coldata) 
pca_plots$clean_norm <- biplot(pcaData, colby = "Genotype", shape = "Engulfment", legendPosition = "right") + ggtitle("Without outliers all counts")
plot(pca_plots$clean_norm)

pcaData <- PCAtools::pca(assay(rld), metadata=coldata) 
pca_plots$clean_rlog <- biplot(pcaData, colby = "Genotype",  shape = "Engulfment", legendPosition = "right") + ggtitle ("Without outliers all counts rlog")

plot(pca_plots$clean_rlog )

means <- apply(assay(rld), 1, mean)
means <- sort(means, decreasing = TRUE)
means <- means[1:(ifelse(length(means) < 12000 ,yes = length(means), no = 12000))]
filt_vector <- rownames(rld) %in% names(means) 
rld_12k <- rld[filt_vector,]

pcaData <- PCAtools::pca(assay(rld_12k), metadata=coldata) 
pca_plots$rld_12k <- biplot(pcaData,  shape = "Genotype", colby = "treatment", legendPosition = "right", title = "Without outliers top12k genes rlog")
plot(pca_plots$rld_12k)

library(Biobase)
library(dplyr)

Attaching package: ‘dplyr’

The following object is masked from ‘package:Biobase’:

    combine

The following object is masked from ‘package:matrixStats’:

    count

The following objects are masked from ‘package:GenomicRanges’:

    intersect, setdiff, union

The following object is masked from ‘package:GenomeInfoDb’:

    intersect

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    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from ‘package:S4Vectors’:

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from ‘package:BiocGenerics’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:data.table’:

    between, first, last

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

fData <- data.frame(ncbiRefSeq = rownames(all_counts))

rownames(fData) <- fData$ncbiRefSeq
## do annotaiton that will be displayed in phantasus
## your annotation can be different from the example

pData <- as.data.frame(meta)
rownames(pData) <- colnames(all_counts)

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

other_plots <- list()
library(edgeR)

Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:DESeq2’:

    plotMA

The following object is masked from ‘package:BiocGenerics’:

    plotMA

norm_counts <- log1p(cpm(all_counts))
norm_counts <- as.data.frame(all_counts)
colnames(all_counts) <- colnames(all_counts)
findoutlier <- function(x) {
  return(x < quantile(x, .25) - 1.5*IQR(x) | x > quantile(x, .75) + 1.5*IQR(x))
}
coldata$treatment <- paste(coldata$Engulfment, coldata$time, sep= "_")
dat <- data.frame( t(norm_counts[rowdata$ncbiRefSeq == "Ptpn11",]),coldata$Genotype, coldata$treatment) 
colnames(dat) <- c("Ptpn11", "genotype", "treatment")
rownames(dat) <- rownames(coldata)
dat$sample <- rownames(dat)
library(dplyr)

Attaching package: ‘dplyr’

The following object is masked from ‘package:Biobase’:

    combine

The following object is masked from ‘package:matrixStats’:

    count

The following objects are masked from ‘package:GenomicRanges’:

    intersect, setdiff, union

The following object is masked from ‘package:GenomeInfoDb’:

    intersect

The following objects are masked from ‘package:IRanges’:

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from ‘package:S4Vectors’:

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from ‘package:BiocGenerics’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:data.table’:

    between, first, last

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

dat <- dat %>% group_by(genotype, treatment) %>% mutate(outlier = ifelse(findoutlier(Ptpn11), sample, NA))
other_plots$ptpn11 <- ggplot( data =  dat, aes( x = treatment, y = Ptpn11 )) + geom_boxplot(aes(fill = genotype)) + geom_text(aes(label=outlier), na.rm=TRUE, hjust=-.5) + ggtitle("Ptpn11 expression")
plot(other_plots$ptpn11)

just compare KO vs WT

de_plots <- list()



dds_all<- DESeqDataSetFromMatrix(all_counts, colData = coldata, design=~Genotype)
dds_all <- estimateSizeFactors(dds_all)
dds_all <- DESeq(dds_all)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 44 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

#plotDispEsts(dds_alone)


dds_all_res <- results(dds_all, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_all_res$ncbiRefSeq <- rowdata[rownames(dds_all_res),]
dds_all_res <- as.data.frame(dds_all_res)

de_plots$all_KOvsWT <- ggplot(dds_all_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_all_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in all samples")
plot(de_plots$all_KOvsWT)

Warning: Removed 13008 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 7875 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_all, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_all_res$log2FoldChange <- cur_shr$log2FoldChange
dds_all_res$lfcSE <- cur_shr$lfcSE

de_plots$all_KOvsWT_apeglm <- 
ggplot(dds_all_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_all_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in all samples(apeglm)")
plot(de_plots$all_KOvsWT_apeglm)

Warning: Removed 13008 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 7875 unlabeled data points (too many overlaps). Consider increasing max.overlaps

compare wt vs KO by eated/uneated

alone_samples <- coldata$Engulfment == 'alone'
alone_coldata <- as.data.frame(coldata[alone_samples,])
rownames(alone_coldata) <- alone_coldata$Samples_Identifier
alone_counts <- all_counts[, alone_samples]
dds_alone <- DESeqDataSetFromMatrix(alone_counts, colData = alone_coldata, design=~Genotype)
dds_alone <- estimateSizeFactors(dds_alone)
dds_alone <- DESeq(dds_alone)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 20 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

#plotDispEsts(dds_alone)


dds_alone_res <- results(dds_alone, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_alone_res$ncbiRefSeq <- rowdata[rownames(dds_alone_res),]
dds_alone_res <- as.data.frame(dds_alone_res)

de_plots$alone_KOvsWT <- ggplot(dds_alone_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone group")
plot(de_plots$alone_KOvsWT)

Warning: Removed 13807 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6716 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_alone, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_alone_res$log2FoldChange <- cur_shr$log2FoldChange
dds_alone_res$lfcSE <- cur_shr$lfcSE

de_plots$alone_KOvsWT_apeglm <- ggplot(dds_alone_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone group(apeglm)")
plot(de_plots$alone_KOvsWT_apeglm)

Warning: Removed 13807 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6716 unlabeled data points (too many overlaps). Consider increasing max.overlaps

alone_2h_samples <- (coldata$Engulfment == 'alone' & coldata$time =='2h')


alone_2h_coldata <- as.data.frame(coldata[alone_2h_samples,])
rownames(alone_2h_coldata) <- alone_2h_coldata$Samples_Identifier
alone_2h_counts <- all_counts[, alone_2h_samples]
dds_alone_2h <- DESeqDataSetFromMatrix(alone_2h_counts, colData = alone_2h_coldata, design=~Genotype)
dds_alone_2h <- estimateSizeFactors(dds_alone_2h)
dds_alone_2h <- DESeq(dds_alone_2h)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

#plotDispEsts(dds_alone)


dds_alone_2h_res <- results(dds_alone_2h, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_alone_2h_res$ncbiRefSeq <- rowdata[rownames(dds_alone_2h_res),]
dds_alone_2h_res <- as.data.frame(dds_alone_2h_res)

de_plots$alone_2h_KOvsWT <- ggplot(dds_alone_2h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_2h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone 2h group")
plot(de_plots$alone_2h_KOvsWT)

Warning: Removed 15133 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6066 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_alone_2h, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_alone_2h_res$log2FoldChange <- cur_shr$log2FoldChange
dds_alone_2h_res$lfcSE <- cur_shr$lfcSE

de_plots$alone_2h_KOvsWT_apeglm <- 
ggplot(dds_alone_2h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_2h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone 2h group(apeglm)")
plot(de_plots$alone_2h_KOvsWT_apeglm)

Warning: Removed 15133 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6068 unlabeled data points (too many overlaps). Consider increasing max.overlaps

#----------
# 4h subset
#---------
alone_4h_samples <- coldata$Engulfment == 'alone' & coldata$time =='4h'
alone_4h_coldata <- as.data.frame(coldata[alone_4h_samples,])
rownames(alone_4h_coldata) <- alone_4h_coldata$Samples_Identifier 
alone_4h_counts <- all_counts[, alone_4h_samples]
dds_alone_4h <- DESeqDataSetFromMatrix(alone_4h_counts, colData = alone_4h_coldata, design=~Genotype)
dds_alone_4h <- estimateSizeFactors(dds_alone_4h)
dds_alone_4h <- DESeq(dds_alone_4h)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

#plotDispEsts(dds_alone)


dds_alone_4h_res <- results(dds_alone_4h, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_alone_4h_res$ncbiRefSeq <- rowdata[rownames(dds_alone_4h_res),]
dds_alone_4h_res <- as.data.frame(dds_alone_4h_res)

de_plots$alone_4h_KOvsWT <- ggplot(dds_alone_4h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_4h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone 4h group")
plot(de_plots$alone_4h_KOvsWT)

Warning: Removed 14826 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6375 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_alone_4h, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_alone_4h_res$log2FoldChange <- cur_shr$log2FoldChange
dds_alone_4h_res$lfcSE <- cur_shr$lfcSE

de_plots$alone_4h_KOvsWT_apeglm <- 
ggplot(dds_alone_4h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_4h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in alone 4h group(apeglm)")
plot(de_plots$alone_4h_KOvsWT_apeglm)

Warning: Removed 14826 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6373 unlabeled data points (too many overlaps). Consider increasing max.overlaps

# =================
# EATED SAMPLES
# =================
eated_samples <- !alone_samples
eated_coldata <- as.data.frame(coldata[eated_samples,])
rownames(eated_coldata) <- eated_coldata$Samples_Identifier
eated_counts <- all_counts[, eated_samples]
dds_eated <- DESeqDataSetFromMatrix(eated_counts, colData = eated_coldata, design=~Genotype)
dds_eated <- estimateSizeFactors(dds_eated)
dds_eated <- estimateDispersions(dds_eated)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_eated <- DESeq(dds_eated)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 26 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

plotDispEsts(dds_eated)

dds_eated_res <- results(dds_eated, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_eated_res$ncbiRefSeq <- rowdata[rownames(dds_eated_res),]
dds_eated_res <- as.data.frame(dds_eated_res)

de_plots$eated_KOvsWT <- ggplot(dds_eated_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated group")

plot(de_plots$eated_KOvsWT)

Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5850 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_eated, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_eated_res$log2FoldChange <- cur_shr$log2FoldChange
dds_eated_res$lfcSE <- cur_shr$lfcSE


de_plots$eated_KOvsWT_apeglm <- ggplot(dds_eated_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated group(apeglm)")
plot(de_plots$eated_KOvsWT_apeglm)

Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5849 unlabeled data points (too many overlaps). Consider increasing max.overlaps

#------
# 2h subset
#------

eated_2h_samples <- (!alone_samples) & coldata$time =='2h'
eated_2h_coldata <- as.data.frame(coldata[eated_2h_samples,])
rownames(eated_2h_coldata) <- eated_2h_coldata$Samples_Identifier
eated_2h_counts <- all_counts[, eated_2h_samples]
dds_eated_2h <- DESeqDataSetFromMatrix(eated_2h_counts, colData = eated_2h_coldata, design=~Genotype)
dds_eated_2h <- estimateSizeFactors(dds_eated_2h)
dds_eated_2h <- estimateDispersions(dds_eated_2h)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_eated_2h <- DESeq(dds_eated_2h)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

plotDispEsts(dds_eated_2h)

dds_eated_2h_res <- results(dds_eated_2h, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_eated_2h_res$ncbiRefSeq <- rowdata[rownames(dds_eated_2h_res),]
dds_eated_2h_res <- as.data.frame(dds_eated_2h_res)

de_plots$eated_2h_KOvsWT <- ggplot(dds_eated_2h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_2h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated 2h group")

plot(de_plots$eated_KOvsWT)

Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5850 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_eated_2h, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_eated_2h_res$log2FoldChange <- cur_shr$log2FoldChange
dds_eated_2h_res$lfcSE <- cur_shr$lfcSE


de_plots$eated_2h_KOvsWT_apeglm <- ggplot(dds_eated_2h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_2h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated 2h group(apeglm)")
plot(de_plots$eated_KOvsWT_apeglm)

Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5849 unlabeled data points (too many overlaps). Consider increasing max.overlaps

#------
# 4h subset
#------

eated_4h_samples <- (!alone_samples) & coldata$time =='4h'
eated_4h_coldata <- as.data.frame(coldata[eated_4h_samples,])
rownames(eated_4h_coldata) <- eated_4h_coldata$Samples_Identifier
eated_4h_counts <- all_counts[, eated_4h_samples]
dds_eated_4h <- DESeqDataSetFromMatrix(eated_4h_counts, colData = eated_4h_coldata, design=~Genotype)
dds_eated_4h <- estimateSizeFactors(dds_eated_4h)
dds_eated_4h <- estimateDispersions(dds_eated_4h)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_eated_4h <- DESeq(dds_eated_4h)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

plotDispEsts(dds_eated_4h)

dds_eated_4h_res <- results(dds_eated_4h, contrast = c("Genotype","KO", "WT" ), cooksCutoff = FALSE )

dds_eated_4h_res$ncbiRefSeq <- rowdata[rownames(dds_eated_4h_res),]
dds_eated_4h_res <- as.data.frame(dds_eated_4h_res)

de_plots$eated_4h_KOvsWT <- ggplot(dds_eated_4h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_4h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated 2h group")

plot(de_plots$eated_4h_KOvsWT)

Warning: Removed 15055 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5504 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_eated_4h, coef= "Genotype_KO_vs_WT", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_eated_4h_res$log2FoldChange <- cur_shr$log2FoldChange
dds_eated_4h_res$lfcSE <- cur_shr$lfcSE


de_plots$eated_4h_KOvsWT_apeglm <- ggplot(dds_eated_4h_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_eated_4h_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("KO vs WT in eated 4h group(apeglm)")
plot(de_plots$eated_KOvsWT_apeglm)

Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5849 unlabeled data points (too many overlaps). Consider increasing max.overlaps

effects of time

library("ggplot2")
library(ggpubr)
dds_time_alone <- DESeqDataSetFromMatrix(alone_counts, colData = alone_coldata, design=~Genotype + time + Genotype:time)
dds_time_alone <- estimateSizeFactors(dds_time_alone)
dds_time_alone <- estimateDispersions(dds_time_alone)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_time_alone <- DESeq(dds_time_alone)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

dds_time_alone_res <- results(dds_time_alone, name ="GenotypeKO.time4h", cooksCutoff = FALSE )

genes <- rownames(as.data.frame(dds_time_alone_res) %>% slice_min(padj, n = 15, na_rm = TRUE))
effect_count = data.table()
for (genotype in levels(dds_time_alone$Genotype)){
  cur_dds <- dds_time_alone[,dds_time_alone$Genotype == genotype]
 
  for(gene in genes){
      d <- plotCounts(cur_dds, gene=gene, intgroup="time",
                returnData=TRUE)
      d$gene = gene
      d$Genotype = genotype
      effect_count <- rbind(effect_count,d)
  }

}
pal =  get_palette( k = length(genes))
de_plots$alone_time_effect <- ggplot(effect_count, aes(x=time, y=count, colour = gene)) + 
  geom_point(position=position_jitter(w=0.1,h=0)) + geom_line(stat = "summary", fun = median, aes(group = gene)) +
  scale_y_log10(breaks=c(25,100,400)) + facet_wrap(~Genotype) + ggtitle("Time effect in alone samples")
dds_time_alone$sample_Genotype_time <- paste(dds_time_alone$Samples_Identifier,dds_time_alone$Genotype, dds_time_alone$time, sep = "_")

de_plots$alone_time_effect_bar <- barplot(assay(dds_time_alone)[genes,],col = pal, names.arg =dds_time_alone$sample_Genotype_time ,las=2, main="counts of effect genes in alone sampels" )

plot(de_plots$alone_time_effect)

plot(de_plots$alone_time_effect_bar)

# ===========
# eated samples
# ============

dds_time_eated <- DESeqDataSetFromMatrix(eated_counts, colData = eated_coldata, design=~Genotype + time + Genotype:time)
dds_time_eated <- estimateSizeFactors(dds_time_eated)
dds_time_eated <- estimateDispersions(dds_time_eated)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_time_eated <- DESeq(dds_time_eated)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

dds_time_eated_res <- results(dds_time_eated, name ="GenotypeKO.time4h", cooksCutoff = FALSE )

genes <- rownames(as.data.frame(dds_time_eated_res) %>% slice_min(padj, n = 15, na_rm = TRUE))
effect_count = data.table()
for (genotype in levels(dds_time_eated$Genotype)){
  cur_dds <- dds_time_eated[,dds_time_eated$Genotype == genotype]
 
  for(gene in genes){
      d <- plotCounts(cur_dds, gene=gene, intgroup="time",
                returnData=TRUE)
      d$gene = gene
      d$Genotype = genotype
      effect_count <- rbind(effect_count,d)
  }

}
pal =  get_palette( k = length(genes))
de_plots$eated_time_effect<- ggplot(effect_count, aes(x=time, y=count, colour = gene)) + scale_color_manual(values= pal)+ 
  geom_point(position=position_jitter(w=0.1,h=0)) + geom_line(stat = "summary", fun = median, aes(group = gene)) +
  scale_y_log10(breaks=c(25,100,400)) + facet_wrap(~Genotype) + ggtitle("Time effect in eated samples")

dds_time_eated$sample_Genotype_time <- paste(dds_time_eated$Samples_Identifier,dds_time_eated$Genotype, dds_time_eated$time, sep = "_")

de_plots$eated_time_effect_bar <- barplot(assay(dds_time_eated)[genes,],col = pal, names.arg =dds_time_eated$sample_Genotype_time ,las=2, main="counts of effect genes in eated samples" )

plot(de_plots$eated_time_effect)

plot(de_plots$eated_time_effect_bar)

get pathways

library(msigdbr)
library(data.table)
library(fgsea)
library(gridExtra)

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine

The following object is masked from ‘package:Biobase’:

    combine

The following object is masked from ‘package:BiocGenerics’:

    combine

kegg_sets <- msigdbr(species = "Mus musculus", category = "C2",  subcategory = "CP:KEGG")
react_sets <- msigdbr(species = "Mus musculus", category = "C2",  subcategory = "CP:REACTOME")
wiki_sets <-  msigdbr(species = "Mus musculus", category = "C2",  subcategory = "CP:WIKIPATHWAYS")
c2_sets <- rbind(kegg_sets, react_sets,wiki_sets )
c2_sets <- data.table(c2_sets)
c2_sets <- c2_sets[, .(sets = list(gene_symbol)), by = gs_name]
c2_gene_sets <- c2_sets$sets 
names(c2_gene_sets) <- c2_sets$gs_name

hall_sets <- msigdbr(species = "Mus musculus", category = "H")
hall_sets <- data.table(hall_sets)
hall_sets <- hall_sets[, .(sets = list(gene_symbol)), by = gs_name]
hall_gene_sets <- hall_sets$sets 
names(hall_gene_sets) <- hall_sets$gs_name

go_sets <- msigdbr(species = "Mus musculus", category = "C5", subcategory = "GO:BP" )
go_sets <- data.table(go_sets)
go_sets <- go_sets[, .(sets = list(gene_symbol)), by = gs_name]
go_gene_sets <- go_sets$sets 
names(go_gene_sets) <- go_sets$gs_name

library(data.table)
padj_threshold <- 0.05
fgsea_results <- function(cur_table, gene_sets){
   inp_stats <- setNames(cur_table$stat, nm = cur_table$ncbiRefSeq)
   fgsea_res <- fgsea(gene_sets, inp_stats)
   fgsea_res <- fgsea_res[padj <= padj_threshold]
   setorder(fgsea_res, padj)
   if(nrow(fgsea_res) == 0){
     print("!!! NO significant pathways !!!")
   }
   if(nrow(fgsea_res)>10){
        collapsedPathways <- collapsePathways(fgsea_res,
                                      gene_sets, inp_stats)
   mainPathways <- fgsea_res[pathway %in% collapsedPathways$mainPathways][
                         order(-NES), pathway]
   }else{
     mainPathways <- fgsea_res[order(-NES), pathway]
   }

   return( list(full_res = fgsea_res, collapsed =  mainPathways) )
}


library(ggplot2)
perform_PE <- function(de, gene_set, set_name, de_name){
         fgsea_res_path <-  file.path(pe_dir, paste(de_name, set_name,"rds", sep = "."))
         if(file.exists(fgsea_res_path)){
           message(paste(
             "!already exists!", fgsea_res_path, sep = "\n"
           ))
           return(TRUE)
         }
         de  <- de[!is.na(de$stat),]
         print(paste("start :", de_name ))
         res <- fgsea_results(cur_table = de, gene_sets = gene_set)
         saveRDS( object =  res, file = fgsea_res_path)
         return(TRUE)
}

pe_dir <- "/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea"
dir.create(pe_dir)

Warning in dir.create(pe_dir) :
  '/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea' already exists

perform_PE(de  = dds_all_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "all_KOvsWT" )

[1] "start : all_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_all_res, gene_set = go_gene_sets,  set_name = "go", de_name = "all_KOvsWT" )

[1] "start : all_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.47% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.47% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.42% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.42% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_all_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "all_KOvsWT" )

[1] "start : all_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.19% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (9.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "alone_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/alone_KOvsWT.hallmark.rds

[1] TRUE

perform_PE(de  = dds_alone_res, gene_set = go_gene_sets,  set_name = "go", de_name = "alone_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/alone_KOvsWT.go.rds

[1] TRUE

perform_PE(de  = dds_alone_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "alone_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/alone_KOvsWT.kegg_c2.rds

[1] TRUE

perform_PE(de  = dds_eated_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "eated_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/eated_KOvsWT.hallmark.rds

[1] TRUE

perform_PE(de  = dds_eated_res, gene_set = go_gene_sets,  set_name = "go", de_name = "eated_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/eated_KOvsWT.go.rds

[1] TRUE

perform_PE(de  = dds_eated_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "eated_KOvsWT" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/eated_KOvsWT.kegg_c2.rds

[1] TRUE

perform_PE(de  = dds_alone_2h_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "alone_2h_KOvsWT" )

[1] "start : alone_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_2h_res, gene_set = go_gene_sets,  set_name = "go", de_name = "alone_2h_KOvsWT" )

[1] "start : alone_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.32% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.32% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.05% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.05% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.49% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.49% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_2h_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "alone_2h_KOvsWT" )

[1] "start : alone_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_2h_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "eated_2h_KOvsWT" )

[1] "start : eated_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.32% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.32% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_2h_res, gene_set = go_gene_sets,  set_name = "go", de_name = "eated_2h_KOvsWT" )

[1] "start : eated_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.08% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.58% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.58% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.12% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.12% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.54% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.54% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.51% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.51% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.94% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.05% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.05% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.48% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.54% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.54% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (10% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.67% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (11.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (11.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.71% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_2h_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "eated_2h_KOvsWT" )

[1] "start : eated_2h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.12% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.12% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.84% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.89% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.8% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.14% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (12.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_4h_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "alone_4h_KOvsWT" )

[1] "start : alone_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_4h_res, gene_set = go_gene_sets,  set_name = "go", de_name = "alone_4h_KOvsWT" )

[1] "start : alone_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.2% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.6% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.56% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.63% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.68% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.45% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.42% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.42% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.55% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.55% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_alone_4h_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "alone_4h_KOvsWT" )

[1] "start : alone_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.41% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.36% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.57% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.46% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.28% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.35% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.24% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.3% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.26% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (13.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_4h_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "eated_4h_KOvsWT" )

[1] "start : eated_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_4h_res, gene_set = go_gene_sets,  set_name = "go", de_name = "eated_4h_KOvsWT" )

[1] "start : eated_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.43% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.33% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.87% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.17% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.37% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.55% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.55% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.88% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.91% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.34% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.29% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.9% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.66% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.22% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.74% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.85% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.49% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.49% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.77% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.99% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.64% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.04% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.25% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.75% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.62% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (7.38% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.83% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.11% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.16% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.44% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.21% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.58% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (4.58% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.09% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.1% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.96% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.82% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.02% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.53% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.53% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.93% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.95% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.69% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.97% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.31% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (3.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.86% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (5.07% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.72% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (6.98% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.23% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.27% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (2.65% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

perform_PE(de  = dds_eated_4h_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "eated_4h_KOvsWT" )

[1] "start : eated_4h_KOvsWT"

Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.73% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.18% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.92% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.01% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.61% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (15.06% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (0.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.78% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.7% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (1.39% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.81% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.79% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (14.76% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.

[1] TRUE

compare eated vs uneated by KO/WT

KO_samples <- coldata$Genotype == 'KO'
KO_coldata <- as.data.frame(coldata[KO_samples,])
rownames(KO_coldata) <- KO_coldata$Samples_Identifier
KO_counts <- all_counts[, KO_samples]
dds_KO <- DESeqDataSetFromMatrix(KO_counts, colData = KO_coldata, design=~Engulfment) # TODO HERE
dds_KO <- estimateSizeFactors(dds_KO)
dds_KO <- DESeq(dds_KO)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 15 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

plotDispEsts(dds_KO)

dds_KO_res <- results(dds_KO, contrast = c("Engulfment","eating", "alone" ), cooksCutoff = FALSE )

dds_KO_res$ncbiRefSeq <- rowdata[rownames(dds_KO_res),]
dds_KO_res <- as.data.frame(dds_KO_res)
de_plots$KO_eatedvsalone <- ggplot(dds_KO_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_alone_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("eated vs alone in KO group")

plot(de_plots$KO_eatedvsalone )

Warning: Removed 19483 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6716 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_KO, coef= "Engulfment_eating_vs_alone", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_KO_res$log2FoldChange <- cur_shr$log2FoldChange
dds_KO_res$lfcSE <- cur_shr$lfcSE

de_plots$KO_eatedvsalone_apeglm  <- ggplot(dds_KO_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_KO_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("eated vs alone in KO group(apeglm)")
plot(de_plots$KO_eatedvsalone_apeglm )

Warning: Removed 19483 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1682 unlabeled data points (too many overlaps). Consider increasing max.overlaps

# =================
# EATED SAMPLES
# =================
WT_samples <- !KO_samples
WT_coldata <- as.data.frame(coldata[WT_samples,])
rownames(WT_coldata) <- WT_coldata$Samples_Identifier
WT_counts <- all_counts[, WT_samples]
dds_WT <- DESeqDataSetFromMatrix(WT_counts, colData = WT_coldata, design=~Engulfment)
dds_WT <- estimateSizeFactors(dds_WT)
dds_WT <- estimateDispersions(dds_WT)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

plotDispEsts(dds_WT)

dds_WT <- DESeq(dds_WT)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 39 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing

dds_WT_res <- results(dds_WT, contrast =  c("Engulfment","eating", "alone" ), cooksCutoff = FALSE )

dds_WT_res$ncbiRefSeq <- rowdata[rownames(dds_WT_res),]
dds_WT_res <- as.data.frame(dds_WT_res)
de_plots$WT_eatedvsalone <- ggplot(dds_WT_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_WT_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("eated vs alone in WT group")

plot(de_plots$WT_eatedvsalone)

Warning: Removed 20756 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1062 unlabeled data points (too many overlaps). Consider increasing max.overlaps

cur_shr <- lfcShrink(dds_WT, coef= "Engulfment_eating_vs_alone", type = "apeglm")

using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895

dds_WT_res$log2FoldChange <- cur_shr$log2FoldChange
dds_WT_res$lfcSE <- cur_shr$lfcSE


de_plots$WT_eatedvsalone_apeglm <-ggplot(dds_WT_res, aes(x=log2FoldChange, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=dds_WT_res %>% dplyr::filter(padj < 0.05), aes(label=ncbiRefSeq, color=NULL)) + ggtitle ("eated vs alone in WT group(apeglm)")
plot(de_plots$WT_eatedvsalone_apeglm)

Warning: Removed 20756 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1059 unlabeled data points (too many overlaps). Consider increasing max.overlaps

effects of time

library("ggplot2")
library(ggpubr)
dds_time_KO <- DESeqDataSetFromMatrix(KO_counts, colData = KO_coldata, design=~Engulfment + time + Engulfment:time)
dds_time_KO <- estimateSizeFactors(dds_time_KO)
dds_time_KO <- estimateDispersions(dds_time_KO)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_time_KO <- DESeq(dds_time_KO)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

dds_time_KO_res <- results(dds_time_KO, name ="Engulfmenteating.time4h", cooksCutoff = FALSE )

genes <- rownames(as.data.frame(dds_time_KO_res) %>% slice_min(padj, n = 15, na_rm = TRUE))
effect_count = data.table()
for (engul in levels(dds_time_KO$Engulfment)){
  cur_dds <- dds_time_KO[,dds_time_KO$Engulfment == engul]
 
  for(gene in genes){
      d <- plotCounts(cur_dds, gene=gene, intgroup="time",
                returnData=TRUE)
      d$gene = gene
      d$Engulfment = engul
      effect_count <- rbind(effect_count,d)
  }

}
pal =  get_palette( k = length(genes))

de_plots$KO_time_effect <- ggplot(effect_count, aes(x=time, y=count, colour = gene)) + 
  geom_point(position=position_jitter(w=0.1,h=0)) + geom_line(stat = "summary", fun = median, aes(group = gene)) +
  scale_y_log10(breaks=c(25,100,400)) + facet_wrap(~Engulfment) + ggtitle("Time effect in KO samples")
dds_time_KO$sample_Engulfment_time <- paste(dds_time_KO$Samples_Identifier,dds_time_KO$Engulfment, dds_time_KO$time, sep = "_")
de_plots$KO_time_effect_bar <- barplot(assay(dds_time_KO)[genes,],col = pal, names.arg =dds_time_KO$sample_Engulfment_time ,las=2, main="counts of effect genes in KO sampels" )

plot(de_plots$KO_time_effect)

plot(de_plots$KO_time_effect_bar)

# ===========
# WT samples
# ============

dds_time_WT <- DESeqDataSetFromMatrix(WT_counts, colData = WT_coldata, design=~Engulfment + time + Engulfment:time)
dds_time_WT <- estimateSizeFactors(dds_time_WT)
dds_time_WT <- estimateDispersions(dds_time_WT)

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

dds_time_WT <- DESeq(dds_time_WT)

using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

dds_time_WT_res <- results(dds_time_WT, name ="Engulfmenteating.time4h", cooksCutoff = FALSE )

genes <- rownames(as.data.frame(dds_time_WT_res) %>% slice_min(padj, n = 15, na_rm = TRUE))
effect_count = data.table()
for (engul in levels(dds_time_WT$Engulfment)){
  cur_dds <- dds_time_WT[,dds_time_WT$Engulfment == engul]
 
  for(gene in genes){
      d <- plotCounts(cur_dds, gene=gene, intgroup="time",
                returnData=TRUE)
      d$gene = gene
      d$Engulfment = engul
      effect_count <- rbind(effect_count,d)
  }

}
pal =  get_palette( k = length(genes))
de_plots$WT_time_effect <- ggplot(effect_count, aes(x=time, y=count, colour = gene)) + scale_color_manual(values= pal)+ 
  geom_point(position=position_jitter(w=0.1,h=0)) + geom_line(stat = "summary", fun = median, aes(group = gene)) +
  scale_y_log10(breaks=c(25,100,400)) + facet_wrap(~Engulfment) + ggtitle("Time effect in WT samples")

dds_time_WT$sample_Engulfment_time <- paste(dds_time_WT$Samples_Identifier,dds_time_WT$Engulfment, dds_time_WT$time, sep = "_")
de_plots$WT_time_effect_bar <- barplot(assay(dds_time_WT)[genes,],col = pal, names.arg =dds_time_WT$sample_Engulfment_time ,las=2, main="counts of effect genes in WT samples" )

plot(de_plots$WT_time_effect)

plot(de_plots$WT_time_effect_bar)

 perform_PE(de  = dds_KO_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "KO_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/KO_EatedvsAlone.hallmark.rds

[1] TRUE

 perform_PE(de  = dds_KO_res, gene_set = go_gene_sets,  set_name = "go", de_name = "KO_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/KO_EatedvsAlone.go.rds

[1] TRUE

  perform_PE(de  = dds_KO_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "KO_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/KO_EatedvsAlone.kegg_c2.rds

[1] TRUE

 perform_PE(de  = dds_WT_res, gene_set = hall_gene_sets,  set_name = "hallmark", de_name = "WT_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/WT_EatedvsAlone.hallmark.rds

[1] TRUE

 perform_PE(de  = dds_WT_res, gene_set = go_gene_sets,  set_name = "go", de_name = "WT_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/WT_EatedvsAlone.go.rds

[1] TRUE

 perform_PE(de  = dds_WT_res, gene_set = c2_gene_sets,  set_name = "kegg_c2", de_name = "WT_EatedvsAlone" )

!already exists!
/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/WT_EatedvsAlone.kegg_c2.rds

[1] TRUE

a <- readRDS("/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/fgsea/eated_KOvsWT.hallmark.rds")

fgsea_files <- list.files(pe_dir, pattern = ".rds")
fgsea_all <- data.table()
main_pathways <- c()


for(fgsea_file in fgsea_files){
   fgsea_res <- readRDS(file = file.path(pe_dir,fgsea_file))
   main_pathways <- unique(c(main_pathways, fgsea_res$collapsed))
   fgsea_res <- fgsea_res$full_res
   comparison <- sub(x = fgsea_file, pattern = "(.+)\\.(.+)\\.rds", replacement = "\\1")
   gene_sets <- sub(x = fgsea_file, pattern = "(.+)\\.(.+)\\.rds", replacement = "\\2")
   fgsea_res$comparison <- comparison
   fgsea_res$set_name <- gene_sets
   fgsea_all <- rbind(fgsea_all, fgsea_res)
}

fgsea_all$pathway <- as.factor(fgsea_all$pathway)

library(ggplot2)
library(ggrepel)
one_volcano <- function(fgsea_res,  comparison, set_name ) {
   ggplot(fgsea_res, aes(x=NES, y=-log10(padj), color=padj < 0.05)) +
  geom_point() + theme_bw() + scale_color_manual(values=c("black", "red")) +
  geom_text_repel(data=fgsea_res %>% dplyr::filter(padj < 0.05), aes(label=pathway, color=NULL)) + ggtitle(paste (comparison,set_name, sep = "."))
}


volcano_plots <- list()

comparisons <- unique(fgsea_all$comparison)
set_names <- unique(fgsea_all$set_name)
library(ggplot2)
library(ggrepel)

   for (cond in comparisons){
      for (sname in set_names){
         cur_res <- fgsea_all[comparison == cond & pathway %in% main_pathways & set_name == sname ,  ]
         clust_name <- cur_res$cluster_name[1]
         cur_plot <- one_volcano(cur_res, cond, sname)
         volcano_plots[[cond]][[paste(sname, sep = ".")]] <-  cur_plot
      }

     
  
}

volcano_plots

$alone_KOvsWT
$alone_KOvsWT$go

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$alone_KOvsWT$hallmark

$alone_KOvsWT$kegg_c2

Warning: ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$eated_KOvsWT
$eated_KOvsWT$go

Warning: ggrepel: 128 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$eated_KOvsWT$hallmark

$eated_KOvsWT$kegg_c2

Warning: ggrepel: 44 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$KO_EatedvsAlone
$KO_EatedvsAlone$go

Warning: ggrepel: 171 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$KO_EatedvsAlone$hallmark

$KO_EatedvsAlone$kegg_c2

Warning: ggrepel: 49 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$WT_EatedvsAlone
$WT_EatedvsAlone$go

Warning: ggrepel: 309 unlabeled data points (too many overlaps). Consider increasing max.overlaps

$WT_EatedvsAlone$hallmark

$WT_EatedvsAlone$kegg_c2

Warning: ggrepel: 123 unlabeled data points (too many overlaps). Consider increasing max.overlaps

library(stringr)
get_one_dot_plot <- function(fgsea_res,  gene_set){
   data <- fgsea_res[gene_set == gene_set, .(pathway,comparison, NES, padj)]
   print(paste("unique pathways: ",length(unique(data$pathway))))
   # plot: dot plot
   if (gene_set == "halmark"){
     data$pathway_name <- str_sub(data$pathway,1, 30)
   } else {
      data$pathway_name <- data$pathway
   }
   ggplot(data = data, aes(x = comparison, y = pathway_name, 
                        color = NES , size = -log10(padj))) + 
   geom_point() +
   scale_color_gradient(low = "blue", high = "red") +
   theme_bw() + 
   ylab("") + 
   xlab("") + 
   ggtitle( paste( gene_set, "pathways")) +  theme(axis.text.x = element_text(angle = 45, vjust = 0.5))
   }

dot_plots <- list()

for (geneset in unique(fgsea_all$set_name)){
       fgsea_all %>% filter(pathway %in% main_pathways &  padj < 0.05 & set_name == geneset) %>% 
       arrange(padj) -> cur_fgsea
      cur_plot <- get_one_dot_plot(fgsea_res = cur_fgsea,gene_set = geneset)
      dot_plots[[geneset]] <- cur_plot


}

[1] "unique pathways:  475"
[1] "unique pathways:  33"
[1] "unique pathways:  228"

dot_plots

$go

$hallmark

$kegg_c2

library(rasterpdf)  
plot_dir <- "/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/plots"
dir.create(plot_dir)

Warning in dir.create(plot_dir) :
  '/scratch1/fs1/martyomov/maksim/permanent/rnaseq/shannon_CHO/plots' already exists

raster_pdf(file.path(plot_dir,paste0( "pathways_report_0.05.pdf")), width = 15, height = 75, res = 300)

dot_plots$go
dot_plots$kegg_c2

dev.off()

null device 
          1 

raster_pdf(file.path(plot_dir, "all_report.pdf"), width = 13, height = 8, res = 300)

for(plt in pca_plots){
  plot(plt)
}
for (plt in other_plots){
  plot(plt)
}

for(plt in de_plots){
  plot(plt)
}

Warning: Removed 13008 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 7826 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 13008 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 7826 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 13807 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6652 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 13807 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6657 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15133 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6020 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15133 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6017 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 14826 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6325 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 14826 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6331 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5821 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 14427 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5816 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15715 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 4847 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15715 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 4845 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15055 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5463 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 15055 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 5465 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 19483 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 6657 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 19483 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1676 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 20756 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1053 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: Removed 20756 rows containing missing values or values outside the scale range (`geom_point()`).
Warning: ggrepel: 1045 unlabeled data points (too many overlaps). Consider increasing max.overlaps

plot(dot_plots[["hallmark"]])   

      
  
dev.off()

null device 
          1